I have a Joomla site that uses the Twitter Bootstrap Hover Dropdown Plugin in its template.
After opening a Joomla menu link that shows such an external page, the Bootstrap dropdown-menu looses its functionality.
Now I found out, that the disfunction of the Bootstrap Dropdown Menu is directly caused by the Iframe-Wrapper of Joomla whether I use JQuery or not inside the wrapper.
After loading the Iframe-Wrapper the Bootstrap Dropdown Menu stops to work.
After click on another menu item (that is not linked to an Iframe-Wrapper) the DropDown resumes working normal.